Coordinated Gene Activity in Pattern Sets


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Documentation for package ‘CoGAPS’ version 2.6.0

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CoGAPS-package CoGAPS: Coordinated Gene Analysis Pattern Sets
binaryA 'binaryA' creates a binarized heatmap of the A matrix in which the value is 1 if the value in Amean is greater than threshold * Asd and 0 otherwise
calcCoGAPSStat CoGAPS gene set statistic
calcZ 'calcZ' calculates the Z-score for each element based on input mean and standard deviation matrices
CoGAPS 'CoGAPS' calls the C++ MCMC code through gapsRun and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix and then calls calcCoGAPSStat to estimate gene set activity with nPerm set to 500
computeGeneGSProb CoGAPS gene membership statistic
gapsInterPattern 'gapsInterPattern' calculates statistics for measuring the distance between patterns based on genes associated with the patterns
gapsIntraPattern 'gapsIntraPattern' generates statistics for the similarity of gene expression vectors within a pattern
gapsMapRun 'gapsMapRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix; as opposed to gapsRun, this method takes an additional input specifying set patterns in the P matrix
gapsMapTestRun 'gapsMapTestRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix; as opposed to gapsRun, this method takes an additional input specifying set patterns in the P matrix. Test procedures allow for the returning of the matrix and atomic information for A and P during each step of the equilibration and sampling.
gapsRun 'gapsRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix
gapsTestRun 'gapsTestRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix. Test procedures allow for the returning of the matrix and atomic information for A and P during each step of the equilibration and sampling. .
geneGSProb CoGAPS gene membership statistic
GIST.D Sample GIST gene expression data from Ochs et al. (2009).
GIST.S Sample GIST gene expression data from Ochs et al. (2009).
GSets Simulated dataset to quantify gene set membership.
plotAtoms 'plotAtoms' a simple plot of the number of atoms from one of the vectors returned with atom numbers
plotDiag 'plotDiag' plots a series of diagnostic plots
plotGAPS Plotter for GAPS decomposition results
plotP 'plotP' plots the P matrix in a line plot with error bars
plotSmoothPatterns Plot loess smoothed CoGAPS patterns
reorderByPatternMatch Match two sets of patterns found with CoGAPS
residuals 'residuals' calculate residuals and produce heatmap
SimpSim.A Simulated data
SimpSim.D Simulated data
SimpSim.P Simulated data
SimpSim.S Simulated data
tf2ugFC Gene sets defined by transcription factors defined from TRANSFAC.